if you run the ant task "deploy" all the files from the theme parent are getting copied over. Now copy the ones you want to modify to the _diffs folder using the same folder structure. After you've done your modifications re-run the ant call again to see the changes in the portal.

tools/theme_impl is just the project template, it doesn't know anything about the parent themes.

When you create your theme project, you get a build.xml file. Inside of that file you declare the parent theme for the project. It defaults to "_styled", but you can change it to "_unstyled" or "classic". If you want to use another theme from your themes folder, you just change it to "../local-theme-dir".